Methods for Increasing the Selective Efficacy of Gene Therapy Using CAR Peptide and Heparan-Sulfate Mediated Macropinocytosis

ABSTRACT

Disclosed are compositions and methods for triggering disease selective macropinocytosis. The compositions can serve as a marker of disease activity and as a trigger of enhanced macropinocytosis in tissues undergoing disease remodeling such as wound healing, cancer, PAH, inflammation, diabetes, Crohn&#39;s disease, ulcerative colitis, ankylosing spondylitis, diseases of the endometrium, psoriasis, irritable bowel syndrome, arthritis, fibrotic disorders, interstitial cystitis, autoimmune diseases, asthma, acute lung injury, and adult respiratory distress syndrome. The compositions can also serve as a receptor for disease selective cell penetrating peptides in the cells and extracellular matrix of diseased tissues.

RELATED APPLICATIONS

This application is a continuation application claiming priority to U.S.application Ser. No. 15/472,182 filed Mar. 28, 2017, which is adivisional application claiming priority from United States NationalStage application Ser. No. 14/649,455, filed Jun. 3, 2015, now U.S. Pat.No. 9,603,890, claiming priority under 35 U.S.C. 371 from InternationalPatent Application No. PCT/US13/72768 filed on Dec. 3, 2013, whichclaims priority from U.S. Provisional Application No. 61/732,859, filedon Dec. 3, 2012, the contents of which are hereby incorporated byreference herein.

FIELD OF THE INVENTION

The present invention relates generally to the field of molecularmedicine, and specifically to cell and tissue targeting peptides.

BACKGROUND OF THE INVENTION

Cell penetrating peptides were first discovered through efforts todescribe how HIV (Human Immunodefficiency Virus) enters cells (Frankel1988, Green 1988). This led to the discovery of the TAT (Trans-Activatorof Transcription) protein encoded as the TAT gene within the HIV-1 virusas the protein responsible for cell penetration and the identificationof the protein transduction domain, YGRKKRRQRRR, as the first cellpenetrating peptide capable of entering the cell membrane (Lindsay 2002,Wadia 2003, Snyder 2004). Since the discovery of the TAT transductiondomain, other cell penetrating peptides have been discovered (Saalik2004).

Cell penetrating peptides have proven to be a useful tool for thedelivery of proteins, small molecule drugs, antibodies, and othertherapeutic compounds into cells and are currently being tested inclinical trials (Johnson 2011). Cell penetrating homing peptides haveproven to be even more useful in that they can penetrate cellsselectively by tissue type or areas of disease (Ruoslahti 2000, Kaplan2005, Nishimura 2008).

While most cell penetrating peptides have been conjugated orelectrostatically bound to the desired therapeutic payload (Niesner2002, Brooks 2005), recent experiments have described the ability of adisease homing, cell-penetrating peptide CARSKNKDC (CAR) to enhance theability of co-administered vasodilators (fasudil, Y-27632, imatinib, andsildenafil) to selectively lower pulmonary pressure in animal models ofpulmonary arterial hypertension (PAH) (PCT/US11/26535) and additionalexperiments by Järvinen and Ruoslahti have described CAR's ability byitself to promote wound healing (U.S. patent application Ser. No.13/406,699).

However, the mechanism by which CAR enables the selective uptake ofco-administered drugs and promotes wound healing has not been previouslydescribed. Furthermore the receptor to which CAR homes to is yet to beidentified.

There is a need to understand the mechanism by which CAR works, and thereceptor to which it binds. The benefits of identifying the mechanismare numerous, including developing novel diagnostic preparations used toaid in the development of new treatments for a variety of diseases.Identification of the receptor and understanding the related mechanismof action will lead to novel disease applications of cell penetratingpeptides.

SUMMARY OF THE INVENTION

Heparan sulfate is a sulfated polysaccharide that is found on the cellsurface and extracellular matrix of all human cells. It interacts with avariety of proteins and is thus involved in numerous biologicalprocesses such as growth and development. Heparan sulfate's functioncritically depends on the number and the position of sulfate groups,which modulate the binding sites for proteins such as growth factors,cytokines, receptors, enzymes, and inhibitors. However, little is knownabout their roles both in vitro and in vivo.

Disclosed herein is a heparan sulfate moiety, 2-O-sulfo-α-L-iduronicacid-2-deoxy-2-acetamido-α-D-glucopyranosyl (IdoA2S-GlcNS), capable oftriggering disease selective macropinocytosis. The moiety disclosedherein can serve as a marker of disease activity and as a trigger ofenhanced macropinocytosis in tissues undergoing disease remodeling suchas wound healing, cancer, PAH, inflammation, diabetes, Crohn's disease,ulcerative colitis, ankylosing spondylitis, diseases of the endometrium,psoriasis, irritable bowel syndrome, arthritis, fibrotic disorders,interstitial cystitis, autoimmune diseases, asthma, acute lung injury,and adult respiratory distress syndrome. The moiety disclosed herein canalso serve as a receptor for disease selective cell penetrating peptidesin the cells and extracellular matrix of diseased tissues.

Also disclosed herein is a sulfotransferase enzyme, Heparan sulfate2-O-sulfotransferase-1 (HS2ST1), involved in the synthesis ofIdoA2S-GlcNS. The sulfotransferase enzyme disclosed herein can serve asa marker of diseases such as wound healing, cancer, PAH, inflammation,diabetes, Crohn's disease, ulcerative colitis, ankylosing spondylitis,diseases of the endometrium, psoriasis, irritable bowel syndrome,arthritis, fibrotic disorders, interstitial cystitis, autoimmunediseases, asthma, acute lung injury, and adult respiratory distresssyndrome. The sulfotransferase enzyme disclosed herein can also serve asa marker for the need for enhanced macropinocytosis in the tissuesexpressing elevated levels of HS2ST1. Methods of treating diseasescharacterized by elevated HS2ST1 are also disclosed herein.

Alterations in heparan sulfation may be associated with pathologicconditions such as cancer. Heparan sulfate 6-O-sulfotransferases(HS6STs) catalyze the transfer of sulfate groups to the carbon 6position in heparan sulfate. Three isoforms of these enzymes have beendiscovered in humans. Disclosed herein is a Heparan sulfate6-O-sulfotransferase-3, (HS6ST3), which can serve as a marker ofdiseases such as wound healing, cancer, PAH, inflammation, diabetes,Crohn's disease, ulcerative colitis, ankylosing spondylitis, diseases ofthe endometrium, psoriasis, irritable bowel syndrome, arthritis,fibrotic disorders, interstitial cystitis, autoimmune diseases, asthma,acute lung injury, and adult respiratory distress syndrome. Thesulfotransferase enzyme disclosed herein can also serve as a marker forthe need for enhanced macropinocytosis in the tissues expressingelevated levels of HS6ST3. Methods of treating diseases characterized byelevated HS6ST3 are also disclosed herein.

Also disclosed herein is a heparan sulfate degrading enzyme, heparanase(HPSE), involved in the degradation and cleavage of heparan sulfatemoieties. The enzyme disclosed herein can serve as a marker of diseasessuch as wound healing, cancer, PAH, inflammation, diabetes, Crohn'sdisease, ulcerative colitis, ankylosing spondylitis, diseases of theendometrium, psoriasis, irritable bowel syndrome, arthritis, fibroticdisorders, interstitial cystitis, autoimmune diseases, asthma, acutelung injury, and adult respiratory distress syndrome. The enzymedisclosed herein can also serve as a marker for the need for enhancedmacropinocytosis in the tissues expressing elevated levels of HPSE.Methods of treating diseases characterized by elevated HPSE are alsodisclosed herein.

Also disclosed herein are methods for improving the selective efficacyof gene therapy. Disclosed are methods wherein the selective efficacy ofgene therapy is increased in a localized manner for wound healing,cancer, PAH, inflammation, diabetes, Crohn's disease, ulcerativecolitis, ankylosing spondylitis, diseases of the endometrium, psoriasis,irritable bowel syndrome, arthritis, fibrotic disorders, interstitialcystitis, autoimmune diseases, asthma, acute lung injury, and adultrespiratory distress syndrome. The methods of gene therapy diseaseselective enhancement disclosed herein can involve co-administrationwith the gene therapy and can be orally available.

Also disclosed herein are methods of treating diseases characterized bydecreased macropinocytosis by administering a disease selectivemacropinocytosis promoter. The disease characterized by decreasedmacropinocytosis can be wound healing, cancer, PAH, inflammation,diabetes, Crohn's disease, ulcerative colitis, ankylosing spondylitis,diseases of the endometrium, psoriasis, irritable bowel syndrome,arthritis, fibrotic disorders, interstitial cystitis, autoimmunediseases, asthma, acute lung injury, and adult respiratory distresssyndrome and the disease selective macropinocytosis promoter can be acell penetrating peptide. The disease selective macropinocytosispromoters disclosed herein can involve co-administration with the genetherapy and can be orally available.

Additional advantages of the disclosed method and compositions will beset forth in part in the description which follows, and in part will beunderstood from the description, or may be learned by practice of thedisclosed method and compositions. The advantages of the disclosedmethod and compositions will be realized and attained by means of theelements and combinations particularly pointed out in the appendedclaims.

It is to be understood that both the foregoing general description andthe following detailed description are exemplary and explanatory onlyand are not restrictive of the invention as claimed.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated in and constitute apart of this specification, illustrate several embodiments of thedisclosed invention, and together with the description, serve to explainthe principles of the disclosed methods.

FIG. 1 shows the effects of co-administered CAR peptide on gene therapy.CAR peptide was able to exert its disease-selective adjuvant propertiesby allowing enhanced viral delivery and uptake of gene product (MFN2) inan animal model of severe occlusive PAH in rats. (A) Figure showing theeffect of MFN2 GTx administered alone when compared to control anddiseased animal not given MFN2 Gtx. Statistical significance wasexamined using ANOVA (see Supplement for further statisticalinformation). (B) Change in mitofusion-2 mRNA levels relative tocontrol. The results indicate that MFN2 GTx is significantly enhanced inthe presence of CAR peptide. (C) The RV/LV-S ratio returned tonear-normal (non-diseased/control) levels following co-administration ofCAR with MFN2 GTx. (D) mPAP (mmHg) levels in Sugen hypoxia rats.CAR+MFN2 GTx reduced pressure levels more than when MFN2 GTx wasadministered alone.

Adenoviruses were used as viral delivery vectors to incorporate cDNAinserts of MFN2 into rats with severe occlusive pulmonary hypertensioninduced by Sugen injection followed by hypoxia (FIG. 1). The resultsindicated that when administered alone, MFN2 gene therapy brought MFN2mRNA gene expression levels to within normal range (FIG. 1A). Incontrast to the administration of MFN2 GTx alone (MFN2 only), when CARwas co-administered with MFN2 GTx,(MFN2-CAR), MFN2 mRNA expressionlevels were significantly elevated, greater than 7× above both controllevels and MFN2 Gtx levels of MFN2 expression (P=0.001) (FIG. 1B).Additionally, the ratio of right ventricle to left ventricle+septumweight ratio (RV/LV-S ratio) returned to almost normal when CAR wasco-administered with the MFN2 GTx (FIG. 1C). Finally, Sugen hypoxia ratstreated with MFN2 GTx and CAR peptide displayed pulmonary arterialpressure (mPAP) reductions that were significantly larger (P<0.5) thanPAH rats treated only with MFN2 adenovirus gene therapy (FIG. 1D).

FIG. 2 shows the chemical structure of SEQ ID NO:1, CARSKNKDC (CAR).

FIG. 3 shows CAR peptide binding and internalization mechanism ofaction. FIG. 3a shows healthy glycocalyx located on endothelial cellsurface facing the bloodstream. FIG. 3b shows the result of PAH injury.FIG. 3c shows the initiation of heparan sulfate-mediatedmacropinocytosis. FIG. 3d shows vesicle formation and CARinternalization by cells. FIG. 3e shows release of CAR into diseasedcells.

DETAILED DESCRIPTION OF THE INVENTION

The disclosed methods and compositions can be understood more readily byreference to the following detailed description of particularembodiments and the Examples included therein and to the Figures andtheir previous and following description.

Before the present compounds, compositions, articles, devices, and/ormethods are disclosed and described, it is to be understood that theyare not limited to specific synthetic methods of specific recombinantbiotechnology methods unless otherwise specified, or to particularreagents unless otherwise specified, as such may, of course, vary. It isalso to be understood that the terminology used herein is for thepurposes of describing particular embodiments only and is not intendedto be limiting.

Definitions

As used in the specification and the appended claims, the singular forms“a,” “an” and “the” include plural referents unless the context clearlydictates otherwise. Thus, for example, reference to “a pharmaceuticalcarrier” includes mixtures of two or much such carriers, and the like.

Ranges can be expressed herein as from “about” one particular value,and/or to “about” another particular value. When such a range isexpressed, another embodiment includes from the one particular valueand/or to the other particular value. Similarly, when values areexpressed as approximations, by use of the antecedent “about,” it willbe understood that the particular value forms another embodiment. Itwill be further understood that the endpoints of each of the ranges aresignificant both in relation to the other endpoint, and independently ofthe other endpoint. It is also understood that there are a number ofvalues disclosed herein, and that each value is also herein disclosed as“about” that particular value in addition to the value itself. Forexample, if the value “10” is disclosed, then “about 10” is alsodisclosed. It is also understood that when a value is disclosed that“less than or equal to” the value, “greater than or equal to the value”and possible ranges between values are also disclosed, as appropriatelyunderstood by the skilled artisan. For example, if the value “10” isdisclosed the “less than or equal to 10” as well as “greater than orequal to 10” is also disclosed. It is also understood that throughoutthe application, data is provided in a number of different formats, andthat this data, represents endpoints and starting points, and ranges forany combination of the data points. For example, if a particular datapoint “10” and a particular data point 15 are disclosed, it isunderstood that greater than, greater than or equal to, less than, lessthan or equal to, and equal to 10 and 15 are considered disclosed aswell as between 10 and 15. It is also understood that each unit betweentwo particular units are also disclosed. For example, if 10 and 15 aredisclosed, then 11, 12, 13, and 14 are also disclosed.

In this specification and in the claims which follow, reference will bemade to a number of terms which shall be defined to have the followingmeanings:

The term “bioactive agent” refers to a substance which is used inconnection with an application that is therapeutic or diagnostic innature, such as in methods for diagnosing the presence or absence of adisease in a patient and/or in methods for treating a disease in apatient. As to compatible bioactive agents, those skilled in the artwill appreciate that any therapeutic or diagnostic agent may beincorporated in the stabilized dispersions of the present invention. Forexample, the bioactive agent may be selected from the group consistingof antiallergics, bronchodilators, vasodilators, antihypertensiveagents, bronchoconstrictors, pulmonary lung surfactants, analgesics,antibiotics, leukotriene inhibitors or antagonists, anticholinergics,mast cell inhibitors, antihistamines, anti-inflammatories,anti-neoplastics, anesthetics, anti-tuberculars, imaging agents,cardiovascular agents, enzymes, steroids, genetic material, viralvectors, antisense agents, small molecule drugs, proteins, peptides andcombinations thereof. Particularly preferred bioactive agents comprisecompounds which are to be administered systemically (i.e. to thesystemic circulation of a patient) such as small molecule drugs, imagingagents, peptides, proteins or polynucleotides. As will be disclosed inmore detail below, the bioactive agent may be incorporated, blended in,coated on or otherwise associated with the targeting peptide disclosedherein. Particularly preferred bioactive agents for use in accordancewith the invention include anti-allergics, peptides and proteins,bronchodilators, anti-inflammatory agents and anti-cancer compounds foruse in the treatment of disorders involving diseased tissue reflectingaltered heparan sulfate variants specific to said disease. Yet anotherassociated advantage of the present invention is the effective deliveryof bioactive agents administered or combined with a targeting peptide.

As used herein, the term “dendrimer” shall mean repeatedly branched androughly spherical molecules. A dendrimer is typically symmetric around acore and usually adopts a spherical three-dimensional morphology.Dendrimers generally contain three major portions: a core, an innershell and an outer shell. Dendrimers can be synthesized to havedifferent and varying functionality in each of the major portions inorder to control such variables as solubility, thermal stability andattachment of compounds suitable for particular applications.

“Optional” or “optionally” means that subsequently described event orcircumstance may or may not occur, and that the description includesinstances where said event or circumstance occurs and instances where itdoes not.

As used herein, the phrase “other compounds and compositions” is usedbroadly such that “compounds” and “compositions” may mean ananoparticle, a nanoworm, an iron oxide nanoworm, an iron oxidenanoparticle, an albumin nanoparticle, a liposome, a micelle, aphospholipid, a polymer, a microparticle, a fluorocarbon microbubble, atherapeutic agent, a therapeutic protein, a therapeutic compound, atherapeutic composition, a chemotherapeutic agent, a cancerchemotherapeutic agent, a toxin, a cytotoxic agent, Abraxane,paclitaxel, taxol, imatinib, an anti-angiogenic agent, a pro-angiogenicagent, an anti-inflammatory agent, an anti-arthritic agent, a TGF-Binhibitor, decorin, a systemic vasodilator, an anti-coagulant, tissuefactor pathway inhibitor (TFPI), site-inactivated factor VIIa, a B-2agonist, salmeterol, formoterol, N-Acetylcysteine (NAC), SuperoxideDismutase (SOD), a superoxide dismutase mimetic, EUK-8, an endothelin(ET-1) receptor antagonist, a prostacyclin derivative, aphosphodiesterase type 5 inhibitor, Ketoconazole, an antibody, a smallinterfering RNA (siRNA), a microRNA (miRNA), a polypeptide, a nucleicacid molecule, a small molecule, a carrier, a vehicle, a virus, a phage,a viral particle, a phage particle, a viral capsid, a phage capsid, avirus-like particle, a liposome, a micelle, a bead, a nanoparticle, amicroparticle, a detectable agent, a contrast agent, an imaging agent, alabel, a labeling agent, a fluorophore, fluorescein, rhodamine, FAM, aradionuclide, indium-111, technetium-99, carbon-11, or carbon-13 and thelike.

As used herein, the term “peptide” is used broadly to mean peptides,proteins, fragments of proteins and the like. Protein variants andderivatives are well understood by those of skill in the art and in caninvolve amino acid sequence modifications. For example, amino acidsequence modifications typically fall into one or more of three classes:substitutional, insertional or deletional variants. Insertions includeamino and/or carboxyl terminal fusions as well as intrasequenceinsertions of single or multiple amino acid residues. Insertionsordinarily will be smaller insertions than those of amino or carboxylterminal fusions, for example, on the order of one to four residues.Immunogenic fusion protein derivatives, such as those described in theexamples, are made by fusing a polypeptide sufficiently large to conferimmunogenicity to the target sequence by cross-linking in vitro or byrecombinant cell culture transformed with DNA encoding the fusion.Deletions are characterized by the removal of one or more amino acidresidues from the protein sequence. Typically, no more than about from 2to 6 residues are deleted at any one site within the protein molecule.These variants ordinarily are prepared by site specific mutagenesis ofnucleotides in the DNA encoding the protein, thereby producing DNAencoding the variant, and thereafter expressing the DNA in recombinantcell culture. Techniques for making substitution mutations atpredetermined sites in DNA having a known sequence are well known, forexample M13 primer mutagenesis and PCR mutagenesis. Amino acidsubstitutions are typically of single residues, but can occur at anumber of different locations at once; insertions usually will be on theorder of about from 1 to 10 amino acid residues; and deletions willrange about from 1 to 30 residues. Deletions or insertions preferablyare made in adjacent pairs, i.e. a deletion of 2 residues or insertionof 2 residues. Substitutions, deletions, insertions or any combinationthereof may be combined to arrive at a final construct. The mutationsmust not place the sequence out of reading frame and preferably will notcreate complementary regions that could produce secondary mRNAstructure. Substitutional variants are those in which at least oneresidue has been removed and a different residue inserted in its place.

The phrase “substantially identical” means that a relevant sequence isat least 70%, 75%, 80%, 85%, 90%, 92%, 95% 96%, 97%, 98%, or 99%identical to a given sequence. By way of example, such sequences may beallelic variants, sequences derived from various species, or they may bederived from the given sequence by truncation, deletion, amino acidsubstitution or addition. Percent identity between two sequences isdetermined by standard alignment algorithms such as ClustalX when thetwo sequences are in best alignment according to the alignmentalgorithm.

A polypeptide “variant” as referred to herein means a polypeptidesubstantially homologous to a native polypeptide, but which has an aminoacid sequence different from that encoded by any of the nucleic acidsequences of the invention because of one or more deletions, insertionsor substitutions. Variants can comprise conservatively substitutedsequences, meaning that a given amino acid residue is replaced by aresidue having similar physiochemical characteristics. (See Zubay,Biochemistry, Addison-Wesley Pub. Co., (1983)). It is a well-establishedprinciple of protein and peptide chemistry that certain amino acidssubstitutions, entitled “conservative” amino acid substitutions, canfrequently be made in a protein or a peptide without altering either theconformation or the function of the protein or peptide. Such changesinclude substituting any of alanine (A), isoleucine (I), valine (V), andleucine (L) for any other of these amino acids; aspartic acid (D) forglutamic acid (E) and vice versa; glutamine (Q) for asparagine (N) andvice versa; serine (S) for threonine (T) and vice versa; and arginine(R) for lysine (K) and vice versa.

In addition to the known functional variants, there are derivatives ofthe peptides disclosed herein which can also function in the disclosedmethods and compositions. Protein and peptide variants and derivativesare well understood by those of skill in the art and in can involveamino acid sequence modifications. For example, amino acid sequencemodifications typically fall into one or more of three classes:substitutional, insertional or deletional variants. Insertions includeamino and/or carboxyl terminal fusions as well as intrasequenceinsertions of single or multiple amino acid residues. Insertionsordinarily will be smaller insertions than those of amino or carboxylterminal fusions, for example, on the order of one to four residues.Deletions are characterized by the removal of one or more amino acidresidues from the protein or peptide sequence. Typically, no more thanabout from 2 to 6 residues are deleted at any one site within theprotein or peptide molecule. These variants can be prepared bysite-specific mutagenesis of nucleotides in the DNA encoding the proteinor peptide, thereby producing DNA encoding the variant, and thereafterexpressing the DNA in recombinant cell culture, or via solid statepeptide synthesis.

Substitutional variants are those in which at least one residue has beenremoved and a different residue inserted in its place. Substantialchanges in function or immunological identity are made by selectingsubstitutions that are less conservative, i.e., selecting residues thatdiffer more significantly in their effect on maintaining (a) thestructure of the polypeptide backbone in the area of the substitution,for example as a sheet or helical conformation, (b) the charge orhydrophobicity of the molecule at the target site or (c) the bulk of theside chain. The substitutions which in general are expected to producethe greatest changes in the protein properties will be those in which(a) a hydrophilic residue, e.g. seryl or threonyl, is substituted for(or by) a hydrophobic residue, e.g. leucyl, isoleucyl, phenylalanyl,valyl or alanyl; (b) a cysteine or proline is substituted for (or by)any other residue; (c) a residue having an electropositive side chain,e.g., lysyl, arginyl, or histidyl, is substituted for (or by) anelectronegative residue, e.g., glutamyl or aspartyl; or (d) a residuehaving a bulky side chain, e.g., phenylalanine, is substituted for (orby) one not having a side chain, e.g., glycine, in this case, (e) byincreasing the number of sites for sulfation and/or glycosylation.Similarly, the term “conformational homology” may be used herein todefine a sequence which maintains a similar arrangement of amino acidsfrom a conformational perspective to SEQ ID NO:1 or SEQ ID NO:2.

It is understood that the description of conservative mutations andhomology can be combined together in any combination, such asembodiments that have at least 70% homology to a particular sequencewherein the variants are conservative mutations.

As this specification discusses various proteins and protein sequencesit is understood that the nucleic acids that can encode those proteinsequences are also disclosed. This would include all degeneratesequences related to a specific protein sequence, i.e. all nucleic acidshaving a sequence that encodes one particular protein sequence as wellas all nucleic acids, including degenerate nucleic acids, encoding thedisclosed variants and derivatives of the protein sequences. Thus, whileeach particular nucleic acid sequence may not be written out herein, itis understood that each and every sequence is in fact disclosed anddescribed herein through the disclosed protein sequence.

It is understood that there are numerous amino acid and peptide analogswhich can be incorporated into the disclosed compositions. For example,there are numerous D amino acids or amino acids which have a differentfunctional substituent than those discussed above. The opposite stereoisomers of naturally occurring peptides are disclosed, as well as thestereo isomers of peptide analogs. These amino acids can readily beincorporated into polypeptide chains by charging tRNA molecules with theamino acid of choice and engineering genetic constructs that utilize,for example, amber codons, to insert the analog amino acid into apeptide chain in a site specific way (Thorson et al., Methods in Molec.Biol. 77:43-73 (1991), Zoller, Current Opinion in Biotechnology,3:348-354 (1992); Ibba, Biotechnology & Genetic Engineering Reviews13:197-216 (1995), Cahill et al., TIBS, 14(10):400-403 (1989); Benner,TIB Tech, 12:158-163 (1994); Ibba and Hennecke, Bio/technology,12:678-682 (1994) all of which are herein incorporated by reference atleast for material related to amino acid analogs).

Molecules can be produced that resemble peptides, but which are notconnected via a natural peptide linkage. For example, linkages for aminoacids or amino acid analogs can include CH.sub.2NH—, —CH.sub.2S—,—CH.sub.2-CH.sub.2-, —CH.dbd.CH-(cis and trans), —COCH.sub.2-,—CH(OH)CH.sub.2-, and —CHH.sub.2SO— (These and others can be found inSpatola, A. F. in Chemistry and Biochemistry of Amino Acids, Peptides,and Proteins, B. Weinstein, eds., Marcel Dekker, New York, p. 267(1983); Spatola, A. F., Vega Data (March 1983), Vol. 1, Issue 3, PeptideBackbone Modifications (general review); Morley, Trends Pharm Sci (1980)pp. 463-468; Hudson, D. et al., Int J Pept Prot Res 14:177-185 (1979)(—CH.sub.2NH—, CH.sub.2CH.sub.2-); Spatola et al. Life Sci 38:1243-1249(1986) (—CH H.sub.2-S); Hann J. Chem. Soc Perkin Trans. I 307-314 (1982)(—CH—CH—, cis and trans); Almquist et al. J. Med. Chem. 23:1392-1398(1980) (—COCH.sub.2-); Jennings-White et al. Tetrahedron Lett 23:2533(1982) (—COCH.sub.2-); Szelke et al. European Appln, EP 45665 CA (1982):97:39405 (1982) (—CH(OH)CH.sub.2-); Holladay et al. Tetrahedron. Lett24:4401-4404 (1983) (C(OH)CH.sub.2-); and HrubyLife Sci 31:189-199(1982) (—CH.sub.2-S—); each of which is incorporated herein byreference. A particularly preferred non-peptide linkage is —CH.sub.2NH—.It is understood that peptide analogs can have more than one atombetween the bond atoms, such as b-alanine, g-aminobutyric acid, and thelike.

Amino acid analogs and peptide analogs often have enhanced or desirableproperties, such as, more economical production, greater chemicalstability, enhanced pharmacological properties (half-life, absorption,potency, efficacy, etc.), altered specificity (e.g., a broad-spectrum ofbiological activities), reduced antigenicity, and others.

D-amino acids can be used to generate more stable peptides, because Damino acids are not recognized by peptidases and such. Systematicsubstitution of one or more amino acids of a consensus sequence with aD-amino acid of the same type (e.g., D-lysine in place of L-lysine) canbe used to generate more stable peptides. Cysteine residues can be usedto cyclize or attach two or more peptides together. This can bebeneficial to constrain peptides into particular conformations. (Rizoand Gierasch Ann. Rev. Biochem. 61:387 (1992), incorporated herein byreference).

Also disclosed are chimeric proteins containing a disclosed peptidefused to a heterologous protein. In one embodiment, the heterologousprotein can have a therapeutic activity such as cytokine activity,cytotoxic activity or pro-apoptotic activity. In a further embodiment,the heterologous protein can be an antibody or antigen-binding fragmentthereof. In other embodiments, the chimeric protein includes a peptidecontaining the amino acid sequence SEQ ID NO: 1 or SEQ ID NO: 2, or aconservative variant or peptidomimetic thereof, fused to a heterologousprotein. The term “heterologous,” as used herein in reference to aprotein fused to the disclosed peptides, means a protein derived from asource other than the gene encoding the peptide or from which thepeptidomimetic is derived. The disclosed chimeric proteins can have avariety of lengths including, but not limited to, a length of less than100 residues, less than 200 residues, less than 300 residues, less than400 residues, less than 500 residues, less than 800 residues or lessthan 1000 residues.

As used herein, “chimera” and “chimeric” refer to any combination ofsequences derived from two or more sources. This includes, for example,from single moiety of subunit (e.g., nucleotide, amino acid) up toentire source sequences added, inserted and/or substituted into othersequences. Chimeras can be, for example, additive, where one or moreportions of one sequence are added to one or more portions of one ormore other sequences; substitutional, where one or more portions of onesequence are substituted for one or more portions of one or more othersequences; or a combination. “Conservative substitutional chimeras” canbe used to refer to substitutional chimeras where the source sequencesfor the chimera have some structural and/or functional relationship andwhere portions of sequences having similar or analogous structure and/orfunction are substituted for each other. Typical chimeric and humanizedantibodies are examples of conservative substitutional chimeras.

Also disclosed are bifunctional peptides which contain a homing peptidefused to a second peptide having a separate function. Such bifunctionalpeptides have at least two functions conferred by different portions ofthe full-length molecule and can, for example, display anti-angiogenicactivity or pro-apoptotic activity in addition to selective homingactivity.

Also disclosed are isolated multivalent peptides that include at leasttwo subsequences each independently containing a homing molecule (forexample, the amino acid sequence SEQ ID NO: 1 or 2, or a conservativevariant or peptidomimetic thereof). The multivalent peptide can have,for example, at least three, at least five or at least ten of suchsubsequences each independently containing a homing molecule (forexample, the amino acid sequence of SEQ ID NO: 1 or 2, or a conservativevariant or peptidomimetic thereof). In particular embodiments, themultivalent peptide can have two, three, four, five, six, seven, eight,nine, ten, fifteen or twenty identical or non-identical subsequences. Ina further embodiment, the multivalent peptide can contain identicalsubsequences, which consist of a homing molecule (for example, the aminoacid sequence SEQ ID NO: 1 or 2, or a conservative variant orpeptidomimetic thereof). In a further embodiment, the multivalentpeptide contains contiguous identical or non-identical subsequences,which are not separated by any intervening amino acids. In yet furtherembodiments, the multivalent peptide can be cyclic or otherwiseconformationally constrained. In one example, the peptide can becircularized or cyclized via a disulfide bond.

The term “peptidomimetic,” as used herein, means a peptide-like moleculethat has the activity of the peptide upon which it is structurallybased. Such peptidomimetics include chemically modified peptides,peptide-like molecules containing non-naturally occurring amino acids,and peptoids and have an activity such as selective homing activity ofthe peptide upon which the peptidomimetic is derived (see, for example,Goodman and Ro, Peptidomimetics for Drug Design, in “Burger's MedicinalChemistry and Drug Discovery” Vol. 1 (ed. M. E. Wolff; John Wiley & Sons1995), pages 803-861).

If desired, an isolated peptide, or a homing molecule as discussedfurther elsewhere herein, can be cyclic or otherwise conformationallyconstrained. As used herein, a “conformationally constrained” molecule,such as a peptide, is one in which the three-dimensional structure ismaintained substantially in one spatial arrangement over time.Conformationally constrained molecules can have improved properties suchas increased affinity, metabolic stability, membrane permeability orsolubility. Methods of conformational constraint are well known in theart and include cyclization as discussed further elsewhere herein.

As used herein in reference to a peptide, the term “cyclic” means astructure including an intramolecular bond between two non-adjacentamino acids or amino acid analogues. The cyclization can be affectedthrough a covalent or non-covalent bond. Intramolecular bonds include,but are not limited to, backbone to backbone, side-chain to backbone andside-chain to side-chain bonds. A preferred method of cyclization isthrough formation of a disulfide bond between the side-chains ofnon-adjacent amino acids or amino acid analogs. Residues capable offorming a disulfide bond include, for example, cysteine (Cys),penicillamine (Pen), .beta.,.beta.-pentamethylene cysteine (Pmc),.beta.,.beta.-pentamethylene-.beta.-mercaptopropionic acid (Pmp) andfunctional equivalents thereof.

Throughout this application, various publications are referenced. Thedisclosures of these publications in their entireties are herebyincorporated by reference into this application in order to or morefully describe the state of the art to which this pertains. Thereferences disclosed are also individually and specifically incorporatedby reference herein for the material contained in them that is discussedin the sentence in which the reference is relied upon.

It is understood that the disclosed method and compositions are notlimited to specific synthetic methods, specific analytical techniques,or to particular reagents unless otherwise specified, and, as such, mayvary. It is also to be understood that the terminology used herein isfor the purpose of describing particular embodiments only and is notintended to be limiting.

Disclosed herein are peptides that enable intracellular delivery, exitand tissue penetration of compositions. The delivery can be targeted tocells or tissues of interest, such as tumors, regenerating tissue, sitesof injury, surgical sites, tumor vasculature, sites of tumorangiogenesis, sites of inflammation, sites of arthritis, lung tissue,PAH lung vasculature, PAH lesions, remodeled pulmonary arteries, andinterstitial space of lungs. Internalization of compositions (includingnanoparticles, drugs, detectable markers, and other compounds) and theirpayload into target cells and penetration into target tissue canincrease the efficiency of the targeting and the effectiveness of thepayload.

Described herein is a peptide identified as CARSKNKDC (CAR, SEQ ID NO:1). Also described herein is a truncated form of CAR (CARSKNK; tCAR; SEQID NO: 2). It was discovered that the truncated peptide is more potentfor cell internalization and tissue penetration than the parent peptideCAR. These properties make tCAR a useful tool for targeted delivery oftherapeutic and diagnostic agents to breast cancers and perhaps othertypes of tumors as well.

The disclosed tCAR peptides can be specific for a particularpathological lesion or an individual tissue. Examples include tumors,wounded tissue, diseased lung tissue, and fibrotic tissue. The abilityof compositions to penetrate into the extravascular space is a majorfactor limiting the targeting efficacy of compositions in vivo. It hasbeen discovered that a truncated form of the CAR homing peptide mediateshighly efficient internalization of phage and free peptides into cells.

It has also been discovered that tCAR peptides specifically increase thepenetration of drugs into tumors, wounded or injured tissue,regenerating tissue, injured, diseased, or fibrotic lung tissue, andother cells and tissues. Disclosed are homing peptides that specificallyincrease the penetration of compounds and compositions intovasculatures, tissues, and cells targeted by tCAR peptides. Thesepeptides specifically home to target tissues, penetrate tissue, andinternalize into cells. Payloads attached to these peptides, includingdrug, fluorophore, nanoparticle, and the like, accumulate in targetedtissues and penetrate deep into the extravascular tissues, such asextravascular tumor tissues. However, it has also been discovered thatthe payload does not need to be coupled to or associated with the tCARpeptide. The free tCAR peptide specifically induces tissue permeabilityin the targeted tissues, allowing a co-injected drug, nanoparticle, andthe like, to extravasate and penetrate into the targeted tissue. Thissame effect can be achieved with any cells and tissue suitable for tCARinternalization.

The disclosed enhancement of internalization and tissue penetration hasbroad application. Using the disclosed methods, the effective targeting,delivery, and penetration of any drug, compound or composition can beaugmented and enhanced. The effect of the disclosed methods has severalsignificant implications. First, drugs and other compounds andcompositions can be delivered to cells and tissues of interest at higherconcentrations than is possible in standard therapy. This is a result ofthe increased internalization and tissue penetration mediated by thedisclosed peptides. This is particularly significant because the amountof drug that can be administered is generally limited by side effects.Increasing the drug concentration at the target without increasing theamount of drug administered can thus extend and enhance theeffectiveness of any known or future drugs and therapeutics. When usingthe disclosed methods, the increase in drug concentration only occurs intarget cells and tissues and not in non-target tissues. In such cases,the efficacy of the treatment can be increased, while side effects canremain the same. Second, the dose or amount of drug or other compound orcomposition can be reduced without compromising the efficacy of thetreatment. The disclosed methods would result in the same drugconcentration at the target cell or tissue even though the amount ofdrug administered is less. Third, because the adjuvant peptide and thedrug, imaging agent, or other compound or composition need not becoupled to one another, a validated and approved peptide can be used toaugment any drug, imaging agent, or other compound or composition.

It is understood that one way to define the variants and derivatives ofthe disclosed proteins herein is through defining the variants andderivatives in terms of homology/identity to specific known sequences.For example, SEQ ID NO: 2 sets forth a particular sequence of tCAR.Specifically disclosed are variants of these and other peptides hereindisclosed which have at least, 70% or 75% or 80% or 85% or 90% or 95%homology to the stated sequence. Wherein a sequence is said to have atleast about 70% sequence identity, it is understood to also have atleast about 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99%, or 100% sequence identity.

It is also understood that variants and derivatives of the disclosedproteins herein may be defined by defining the variants and derivativesin terms of binding affinity to specific known sequences. For example,IdoA2S-GlcNS is a heparin sulfate moiety that when bound by CAR triggersmacropinocytosis. Specifically disclosed are variants of CAR which haveat least 60% or greater binding affinity to IdoA2S-GlcNS. Wherein a CARvariant is said to have at least about 60% binding affinity, it isunderstood to also have about 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99%, or 100% binding affinity.

Previously, cell-surface heparan sulfate (HS) has been shown to benecessary for both CAR binding and internalization. When treated withheparinase I, binding of CAR to Chinese hamster ovary cells was greatlyreduced. This suggested CAR's specific binding and internalization ismediated by the presence of HS moieties at the surface of the targetcell. However the specific HS moiety to which CAR was binding was notspecifically identified by this experiment.

In order to identify CAR's receptor additional information was required.Since previous studies have described CAR homing to pulmonaryhypertensive arteries, it was deduced that the receptor for CAR must bepresent in PAH. It was further deduced that important clues to CAR'sreceptor could be found in PAH gene expression data.

In a surgical shunt model of PAH, elevated gene expression levels ofHPSE, a substrate specific enzyme were found. HPSE is responsible forthe cleavage of specific HS moieties (Peterson 2010). Since high levelsof HPSE were found in PAH, but CAR bound strongly in PAH, we canconclude HPSE does not inhibit CAR binding and furthermore, the specificHS receptor to which CAR binds is not cleaved by HPSE. However, sinceheparinase I reduced CAR binding, CAR's HS receptor is cleaved byheparinase I.

Interestingly, heparinase I, the enzyme found to inhibit CAR binding,and HPSE do not have the same HS substrate specificity, and one HSmoiety in particular, IdoA2S-GlcNS, is cleaved by heparinase I (Wei2005) but not HPSE. Our PAH gene expression data also revealed extremelyelevated levels of the heparan sulfate 2-O-sulfotransferase 1 (HS2ST1)gene, which encodes the HS2ST1 enzyme and is necessary for synthesis ofthe IdoA2S-GlcNS HS moiety, further suggesting that IdoA2S-GlcNS ispresent at elevated levels in PAH and is likely the CAR receptor.

Since high levels of HPSE were found in PAH, it is likely that CAR wouldalso be useful for treating other diseases characterized by high levelsof HPSE such as tumors, chronic inflammatory diseases, atherosclerosis,coronary artery disease, colitis, inflammatory bowel disorders,diabetes, arterial thrombosis, stent thrombosis, glomerular diseases,wound healing, and endometrial disorders. CAR has already demonstratedits utility in wound healing and homing properties to tumors furthersuggesting that CAR would be useful for treating other diseasescharacterized by elevated HPSE levels.

One possible mechanism by which CAR could facilitate the selectiveuptake of co-administered drugs is through heparan sulfate-mediatedmacropinocytosis. Macropinocytosis is a form of endocytosis that allowsfor the regulated internalization of extracellular solute molecules (Lim2011). Studies have described the role of heparan sulfate as thereceptor for lipid raft-dependent macropinocytotic internalization, andmacropinocytosis has also been shown to underlie the internalization ofother cationic cell-penetrating peptides (Fan 2007). Heparan sulfatemediated macropinocytosis could explain CAR's ability to increase thelocalized concentration of co-administered drugs without requiring thedrugs to be conjugated to CAR as well as CAR's ability to promote woundhealing.

Heparan sulfate-mediated macropinocytosis is a non-clathrin,non-caveolin, lipid raft-dependent form of endocytosis that allows forthe regulated internalization of extracellular solute molecules (Lim2011). HS-mediated macropinocytosis is utilized by various cationiccell-penetrating peptides (Fan 2007), and is a plausible mechanism ofaction to explain both CAR's ability to accelerate wound healing as wellas CAR's ability to increase the localized concentration ofco-administered drugs in diseased tissues. Wound healing could beaccelerated through CAR administration by the selective binding of CARto the wounded area, triggering enhanced macropinocytosis in the woundedtissues. This accelerated macropinocytosis would lead to an increaseduptake of molecules involved in the body's wound healing response suchas cytokines and growth factors. Similarly, the pulmonary selectivevasodilation observed in animal models of PAH when CAR isco-administered with vasodilators could also be explained by thismechanism of action. CAR administration and selective binding to thearea of disease would enhance HS-mediated macropinocytosis, resulting inincreased localized uptake of vasodilatory drugs in the diseasedpulmonary arteries and selective dilation of pulmonary vasculature.

CAR could also facilitate the selective treatment of other diseases inwhich CAR displays homing activity alone or in combination with othertherapies by selectively increasing macropinocytosis in diseased tissuescharacterized by elevated levels of HPSE.

Diabetes, for example, is marked by elevated levels of HPSE (Shafat2011, Katz 2002, Ziolkowski 2012), and the HS moiety to which CAR bindsshould also be present in insulin-resistant tissues in diabetes. In thiscase, CAR should preferentially home to inflamed, insulin-resistanttissue damaged by diabetes, and induce HS-mediated macropinocytosis uponbinding specifically to the diseased tissue. This will lead to increasedglucose uptake and/or improved localized performance of insulin or otherdiabetes medications at the site of inflammation and insulin resistance.Interestingly, reduced macropinocytosis is a hallmark of macrophagesfrom diabetic animal models (Guest 2008). Selectively increasingmacropinocytosis in inflamed tissues associated with diabetes would bean additional benefit of CAR administration in diabetes.

Further evidence of the plausibility of macropinocytosis as themechanism of action for CAR is found in a recent experiment combiningCAR with gene therapy. Based on the demonstrated success of CAR peptideas a disease-selective adjuvant that can be used with variousco-administered therapeutic agents, we further sought to assess CAR'shoming potential in gene therapy (GTx). Previous efforts to increase theselectivity and delivery of gene therapy vectors using cell penetratingpeptides have required that the peptide be covalently orelectrostatically bound to the gene therapy vector (Yao 2012). But thisapproach has often resulted in suboptimal results.

The MFN2 gene encodes the mitofusion-2 protein, which is a mitochondrialmembrane protein that participates in mitochondrial fusion. Mitofusion-2contributes to the maintenance and operation of the mitochondrialnetwork, and is involved in the regulation of vascular smooth musclecell (VSMC) proliferation. MFN2 expression is down-regulated in vascularproliferative disorders such as cancer and pulmonary hypertension, andMFN2 overexpression can attenuate the proliferation of VSMCs. Successfuldelivery and uptake of the MFN2 gene via adenovirus delivery vector intodiseased cells results in increased expression of the mitofusion-2protein, regulation of VSMC proliferation, and a subsequent decrease indisease indicators. We hypothesized that CAR peptide could improve thedisease-selective targeting and localization of adenoviruses containingthe MFN2 gene. Better localization and targeting of MFN2 gene therapyshould result in increased MFN2 mRNA levels, improved mitochondrialfunction, and a reduction in pulmonary arterial pressure.

When we compare the results of the gene therapy experiment with theco-administration effect we see that CAR increased selectivevasodilation approximately 2×, and co-administered drug concentration2×, but gene therapy transfected gene expression increased 7×. Onepossible reason why gene therapy was selectively enhanced 7× while drugselectivity was only enhanced 2× is the mechanism of action by whichadenoviruses transfect cells through the same lipid raft dependentmacropinocytosis mechanism we are proposing for CAR's internalization.Since CAR stimulates macropinocytosis in the target tissues, thelocalized effects of gene therapy transfection are more enhanced by theco-administration of CAR than drug co-administration in which CARstimulates macropinocytosis in the target tissues to increase localizeddrug levels. The increased enhancement of gene therapy versus drugco-administration further supports lipid raft dependent macropinocytosisas CAR's mechanism for cell penetration.

Taken together, these data identify a specific HS moiety (IdoA2S-GlcNS)as a possible receptor for CAR that could be present in pulmonaryhypertensive tissues in which many of the HS moieties have been cleavedby HPSE, which is over-expressed in PAH. We further hypothesize thatheparan sulfate-mediated macropinocytosis could be a plausible mechanismby which CAR binding could trigger the internalization ofco-administered compounds and as a result serve as a selective enhancerof gene therapy and other therapies that utilize macropinocytosis astheir route of cellular entry. CAR's selective triggering ofmacropinocytosis in diseased tissues by itself could also havetherapeutic utility.

In one embodiment, the present invention discloses a peptide thattargets the receptor IdoA2s-GlcNS and selectively penetrates the cellsand extracellular matrix of diseased tissues. In a preferred embodimentthe disease is selected from the group consisting of pulmonaryhypertension, interstitial lung disease, acute lung injury (ALI), acuterespiratory distress syndrome (ARDS), sepsis, septic shock, sarcoidosisof the lung, diabetes, ankylosing spondylitis, psoriasis, diseases ofthe endometrium, pulmonary manifestations of connective tissue diseases,including systemic lupus erythematosus, rheumatoid arthritis,scleroderma, and polymyositis, dermatomyositis, bronchiectasis,asbestosis, berylliosis, silicosis, Histiocytosis X, pneumotitis,smoker's lung, bronchiolitis obliterans, the prevention of lung scarringdue to tuberculosis and pulmonary fibrosis, other fibrotic diseases suchas myocardial infarction, endomyocardial fibrosis, mediastinal fibrosis,myelofibrosis, retroperitoneal fibrosis, progressive massive fibrosis,pneumoconiosis, nephrogenic systemic fibrosis, keloid, arthrofibrosis,adhesive capsulitis, radiation fibrosis, fibrocystic breast condition,liver cirrhosis, hepatitis, liver fibrosis, nonalcoholic fatty liverdisease, nonalcoholic steatohepatitis, sarcoidosis of the lymph nodes,or other organs, inflammatory bowel disease, Crohn's disease, ulcerativecolitis, primary biliary cirrhosis, pancreatitis, interstitial cystitis,chronic obstructive pulmonary disease, pneumoconiosis, autoimmunediseases, angiogenic diseases, wound healing, infections, traumainjuries and systemic connective tissue diseases including systemiclupus erythematosus, rheumatoid arthritis, psoriatic arthritis, juvenileidiopathic arthritis scleroderma, polymyositis, and dermatomyositis. Inanother preferred embodiment, the peptide is CAR. In another preferredembodiment, the peptide is tCAR. In yet another preferred embodiment,the peptide is a variant of CAR with at least 60% binding affinity toIdoA2s-GlcNS.

In one embodiment, the present invention discloses a method of treatinga disease comprising increasing macropinocytosis. In a preferredembodiment, the increase in macropinocytosis is triggered by thepresence of elevated levels of IdoA2s-GlcNS. In another preferredembodiment, the increase in macropinocytosis is triggered by thepresence of elevated levels of heparinase I. In another preferredembodiment, the increase in macropinocytosis is triggered by thepresence of elevated levels of HSPE. In another preferred embodiment,the increase in macropinocytosis is triggered by elevated levels ofHS2ST1. In another preferred embodiment the disease is selected from thegroup consisting of pulmonary hypertension, interstitial lung disease,acute lung injury (ALI), acute respiratory distress syndrome (ARDS),sepsis, septic shock, sarcoidosis of the lung, diabetes, ankylosingspondylitis, psoriasis, diseases of the endometrium, pulmonarymanifestations of connective tissue diseases, including systemic lupuserythematosus, rheumatoid arthritis, scleroderma, and polymyositis,dermatomyositis, bronchiectasis, asbestosis, berylliosis, silicosis,Histiocytosis X, pneumotitis, smoker's lung, bronchiolitis obliterans,the prevention of lung scarring due to tuberculosis and pulmonaryfibrosis, other fibrotic diseases such as myocardial infarction,endomyocardial fibrosis, mediastinal fibrosis, myelofibrosis,retroperitoneal fibrosis, progressive massive fibrosis, pneumoconiosis,nephrogenic systemic fibrosis, keloid, arthrofibrosis, adhesivecapsulitis, radiation fibrosis, fibrocystic breast condition, livercirrhosis, hepatitis, liver fibrosis, nonalcoholic fatty liver disease,nonalcoholic steatohepatitis, sarcoidosis of the lymph nodes, or otherorgans, inflammatory bowel disease, Crohn's disease, ulcerative colitis,primary biliary cirrhosis, pancreatitis, interstitial cystitis, chronicobstructive pulmonary disease, pneumoconiosis, autoimmune diseases,angiogenic diseases, wound healing, infections, trauma injuries andsystemic connective tissue diseases including systemic lupuserythematosus, rheumatoid arthritis, psoriatic arthritis, juvenileidiopathic arthritis scleroderma, polymyositis, and dermatomyositis.

In one embodiment, the present invention discloses a method of treatinga disease comprising increasing macropinocytosis by administering to apatient suffering from a disease a therapeutically effective amount of acell penetrating peptide. In a preferred embodiment, the peptide is CAR.In another preferred embodiment, the peptide is tCAR. In yet anotherpreferred embodiment, the peptide is a variant of CAR with at least 60%binding affinity to IdoA2s-GlcNS. In still another preferred embodimentthe disease is selected from the group consisting of pulmonaryhypertension, interstitial lung disease, acute lung injury (ALI), acuterespiratory distress syndrome (ARDS), sepsis, septic shock, sarcoidosisof the lung, diabetes, ankylosing spondylitis, psoriasis, diseases ofthe endometrium, pulmonary manifestations of connective tissue diseases,including systemic lupus erythematosus, rheumatoid arthritis,scleroderma, and polymyositis, dermatomyositis, bronchiectasis,asbestosis, berylliosis, silicosis, Histiocytosis X, pneumotitis,smoker's lung, bronchiolitis obliterans, the prevention of lung scarringdue to tuberculosis and pulmonary fibrosis, other fibrotic diseases suchas myocardial infarction, endomyocardial fibrosis, mediastinal fibrosis,myelofibrosis, retroperitoneal fibrosis, progressive massive fibrosis,pneumoconiosis, nephrogenic systemic fibrosis, keloid, arthrofibrosis,adhesive capsulitis, radiation fibrosis, fibrocystic breast condition,liver cirrhosis, hepatitis, liver fibrosis, nonalcoholic fatty liverdisease, nonalcoholic steatohepatitis, sarcoidosis of the lymph nodes,or other organs, inflammatory bowel disease, crohn's disease, ulcerativecolitis, primary biliary cirrhosis, pancreatitis, interstitial cystitis,chronic obstructive pulmonary disease, pneumoconiosis, autoimmunediseases, angiogenic diseases, wound healing, infections, traumainjuries and systemic connective tissue diseases including systemiclupus erythematosus, rheumatoid arthritis, psoriatic arthritis, juvenileidiopathic arthritis, scleroderma, polymyositis, and dermatomyositis.

In one embodiment, the present invention discloses a method of treatinga disease characterized by elevated levels of HPSE, the methodcomprising 1) administering a therapeutically effective amount of acompound that binds to IdoA2s-GlcNS; 2) enhancing macropinocytosis inthe target tissue. In a preferred embodiment, the disease is selectedfrom the group consisting of pulmonary hypertension, interstitial lungdisease, acute lung injury (ALI), acute respiratory distress syndrome(ARDS), sepsis, septic shock, sarcoidosis of the lung, diabetes,ankylosing spondylitis, psoriasis, diseases of the endometrium,pulmonary manifestations of connective tissue diseases, includingsystemic lupus erythematosus, rheumatoid arthritis, scleroderma, andpolymyositis, dermatomyositis, bronchiectasis, asbestosis, berylliosis,silicosis, Histiocytosis X, pneumotitis, smoker's lung, bronchiolitisobliterans, the prevention of lung scarring due to tuberculosis andpulmonary fibrosis, other fibrotic diseases such as myocardialinfarction, endomyocardial fibrosis, mediastinal fibrosis,myelofibrosis, retroperitoneal fibrosis, progressive massive fibrosis,pneumoconiosis, nephrogenic systemic fibrosis, keloid, arthrofibrosis,adhesive capsulitis, radiation fibrosis, fibrocystic breast condition,liver cirrhosis, hepatitis, liver fibrosis, nonalcoholic fatty liverdisease, nonalcoholic steatohepatitis, sarcoidosis of the lymph nodes,or other organs, inflammatory bowel disease, crohn's disease, ulcerativecolitis, primary biliary cirrhosis, pancreatitis, interstitial cystitis,chronic obstructive pulmonary disease, pneumoconiosis, autoimmunediseases, angiogenic diseases, wound healing, infections, traumainjuries and systemic connective tissue diseases including systemiclupus erythematosus, rheumatoid arthritis, psoriatic arthritis, juvenileidiopathic arthritis scleroderma, polymyositis, and dermatomyositis. Inanother preferred embodiment, the compound that binds to IdoA2s-GlcNS isCAR. In another preferred embodiment, the compound that binds toIdoA2s-GlcNS is tCAR. In yet another preferred embodiment, the compoundthat binds to IdoA2s-GlcNS is a variant of CAR with at least 60% bindingaffinity to IdoA2s-GlcNS.

In one embodiment, the present invention discloses a method of treatinga disease by inhibiting macropinocystosis by administering atherapeutically effective amount of an irreversible inhibitor ofIdoA2s-GlcNS. In a preferred embodiment, the inhibitor is rationallydesigned using current techniques when the target is known.(http://en.wikipedia.org/wiki/Drug_design) In a preferred embodiment,the disease is selected from the group consisting of pulmonaryhypertension, interstitial lung disease, acute lung injury (ALI), acuterespiratory distress syndrome (ARDS), sepsis, septic shock, sarcoidosisof the lung, diabetes, ankylosing spondylitis, psoriasis, diseases ofthe endometrium, pulmonary manifestations of connective tissue diseases,including systemic lupus erythematosus, rheumatoid arthritis,scleroderma, and polymyositis, dermatomyositis, bronchiectasis,asbestosis, berylliosis, silicosis, Histiocytosis X, pneumotitis,smoker's lung, bronchiolitis obliterans, the prevention of lung scarringdue to tuberculosis and pulmonary fibrosis, other fibrotic diseases suchas myocardial infarction, endomyocardial fibrosis, mediastinal fibrosis,myelofibrosis, retroperitoneal fibrosis, progressive massive fibrosis,pneumoconiosis, nephrogenic systemic fibrosis, keloid, arthrofibrosis,adhesive capsulitis, radiation fibrosis, fibrocystic breast condition,liver cirrhosis, hepatitis, liver fibrosis, nonalcoholic fatty liverdisease, nonalcoholic steatohepatitis, sarcoidosis of the lymph nodes,or other organs, inflammatory bowel disease, crohn's disease, ulcerativecolitis, primary biliary cirrhosis, pancreatitis, interstitial cystitis,chronic obstructive pulmonary disease, pneumoconiosis, autoimmunediseases, angiogenic diseases, wound healing, infections, traumainjuries and systemic connective tissue diseases including systemiclupus erythematosus, rheumatoid arthritis, psoriatic arthritis, juvenileidiopathic arthritis scleroderma, polymyositis, and dermatomyositis.

In one embodiment, the present invention discloses a method of treatinga disease characterized by elevated levels of HS2ST1, the methodcomprising 1) administering a therapeutically effective amount of acompound that binds to IdoA2s-GlcNS; 2) enhancing macropinocytosis inthe target tissue. In a preferred embodiment, the disease is selectedfrom the group consisting of pulmonary hypertension, interstitial lungdisease, acute lung injury (ALI), acute respiratory distress syndrome(ARDS), sepsis, septic shock, sarcoidosis of the lung, diabetes,ankylosing spondylitis, psoriasis, diseases of the endometrium,pulmonary manifestations of connective tissue diseases, includingsystemic lupus erythematosus, rheumatoid arthritis, scleroderma, andpolymyositis, dermatomyositis, bronchiectasis, asbestosis, berylliosis,silicosis, Histiocytosis X, pneumotitis, smoker's lung, bronchiolitisobliterans, the prevention of lung scarring due to tuberculosis andpulmonary fibrosis, other fibrotic diseases such as myocardialinfarction, endomyocardial fibrosis, mediastinal fibrosis,myelofibrosis, retroperitoneal fibrosis, progressive massive fibrosis,pneumoconiosis, nephrogenic systemic fibrosis, keloid, arthrofibrosis,adhesive capsulitis, radiation fibrosis, fibrocystic breast condition,liver cirrhosis, hepatitis, liver fibrosis, nonalcoholic fatty liverdisease, nonalcoholic steatohepatitis, sarcoidosis of the lymph nodes,or other organs, inflammatory bowel disease, crohn's disease, ulcerativecolitis, primary biliary cirrhosis, pancreatitis, interstitial cystitis,chronic obstructive pulmonary disease, pneumoconiosis, autoimmunediseases, angiogenic diseases, wound healing, infections, traumainjuries and systemic connective tissue diseases including systemiclupus erythematosus, rheumatoid arthritis, psoriatic arthritis, juvenileidiopathic arthritis scleroderma, polymyositis, and dermatomyositis. Inanother preferred embodiment, the compound that binds to IdoA2s-GlcNS isCAR. In another preferred embodiment, the compound that binds toIdoA2s-GlcNS is tCAR. In yet another preferred embodiment, the compoundthat binds to IdoA2s-GlcNS is a variant of CAR with at least 60% bindingaffinity to IdoA2s-GlcNS.

In one embodiment, the present invention discloses a method of treatinga disease characterized by reduction in macropinocytosis, the methodcomprising 1) administering a therapeutically effective amount of acompound that binds to IdoA2s-GlcNS; 2) enhancing macropinocytosis inthe target tissue. In a preferred embodiment the disease is selectedfrom the group consisting of pulmonary hypertension, interstitial lungdisease, acute lung injury (ALI), acute respiratory distress syndrome(ARDS), sepsis, septic shock, sarcoidosis of the lung, diabetes,ankylosing spondylitis, psoriasis, diseases of the endometrium,pulmonary manifestations of connective tissue diseases, includingsystemic lupus erythematosus, rheumatoid arthritis, scleroderma, andpolymyositis, dermatomyositis, bronchiectasis, asbestosis, berylliosis,silicosis, Histiocytosis X, pneumotitis, smoker's lung, bronchiolitisobliterans, the prevention of lung scarring due to tuberculosis andpulmonary fibrosis, other fibrotic diseases such as myocardialinfarction, endomyocardial fibrosis, mediastinal fibrosis,myelofibrosis, retroperitoneal fibrosis, progressive massive fibrosis,pneumoconiosis, nephrogenic systemic fibrosis, keloid, arthrofibrosis,adhesive capsulitis, radiation fibrosis, fibrocystic breast condition,liver cirrhosis, hepatitis, liver fibrosis, nonalcoholic fatty liverdisease, nonalcoholic steatohepatitis, sarcoidosis of the lymph nodes,or other organs, inflammatory bowel disease, crohn's disease, ulcerativecolitis, primary biliary cirrhosis, pancreatitis, interstitial cystitis,chronic obstructive pulmonary disease, pneumoconiosis, autoimmunediseases, angiogenic diseases, erectile dysfunction, chronic kidneydisease, wound healing, infections, trauma injuries and systemicconnective tissue diseases including systemic lupus erythematosus,rheumatoid arthritis, psoriatic arthritis, juvenile idiopathic arthritisscleroderma, polymyositis, and dermatomyositis. In another preferredembodiment, the substance administered is a peptide. In anotherpreferred embodiment, the peptide is CAR. In another preferredembodiment, the peptide is tCAR. In another preferred embodiment, thepeptide is a CAR variant with at least 60% binding affinity toIdoA2s-GlcNS. In yet another preferred embodiment, the disease isfurther characterized by elevated levels of one or more of HPSE,heparinase I and HS2ST1.

In one embodiment, the present invention discloses a method of treatinga disease characterized by elevated levels of HPSE and heparinase Icomprising the administration of a therapeutically effective amount of acomposition consisting of:

1) at least one peptide selected from the group consisting of CAR, tCARor a CAR variant with at least 60% binding affinity to IdoA2s-GlcNS; and

2) at least one other therapeutic agent.

In a preferred embodiment, the therapeutic agent is selected from thegroup consisting of small molecules, polypeptides, peptides,peptidomimetics, nucleic acid-molecules, cells and viruses and the like.

In one embodiment, the present invention discloses a method of treatinga disease comprising increasing the localized efficacy of gene therapyby co-administering a therapeutically effective amount of a cellpenetrating peptide and a gene therapy vector. In a preferredembodiment, the peptide is CAR. In another preferred embodiment, thepeptide is tCAR. In another preferred embodiment, the peptide is avariant of CAR with at least 60% binding affinity to IdoA2s-GlcNS.

In one embodiment, the present invention discloses an apparatus fordetermining elevated levels of disease markers wherein the diseasemarkers are selected from the group consisting of HPSE, heparinase I,and HS2ST1. In a preferred embodiment, the apparatus further comprisesimaging agents which bind to the disease markers such that the imagingagents convey the presence and/or level of the disease marker in thesample.

Examples

Recent experiments (Urakami et al. 2011; Toba et al. (in submission))have demonstrated the ability of the pulmonary hypertensive homing,cell-penetrating peptide CARSKNKDC (CAR) (FIG. 2) to enhance the effectsof co-administered vasodilators (fasudil, Y-27632, imatimib, andsildenafil) in selectively lowering pulmonary pressure in animal modelsof pulmonary arterial hypertension (PAH). Here we provide a hypothesisfor CAR's mechanism of action and identify a putative receptor.

Methods

We examined data on enzymatic specificity from the literature andcombined it with genetic expression in a porcine model of pulmonaryhypertension to arrive at a likely target for CAR. In previousexperiments, cell-surface heparan sulfate (HS) was shown to be necessaryfor both CAR binding and internalization (Jarvinen et al. 2007). Whentreated with heparinase I and III, binding of CAR to Chinese hamsterovary cells was greatly reduced. This suggested that CAR's specificbinding and internalization is mediated by the presence of HS moietieson the surface of the target cell.

20-30 kg Yucatan Micropigs underwent surgical anastomosis of the leftpulmonary artery to the descending aorta, resulting in pulmonaryarterial hypertension (Rothman et al. 2011). Endovascular samples wereobtained from 2-3 mm arteries with an endoarterial biopsy catheter atbaseline (prior to surgery), and from the hypertensive left lung 7, 21,60 and 180 days after surgery. RNA was isolated from biopsy samples andloaded into an Affymetrix GeneChip Porcine Whole Genome Array containing20, 201 Sus scrofa genes. Gene expression level differences wereanalyzed using GeneSpring, and gene expression fold changes relative tobaseline were calculated (Rothman et al. 2013).

Results/Hypothesis

In a surgical shunt model of PAH, we found elevated gene expressionlevels of heparanase, a substrate specific enzyme responsible for thecleavage of specific HS moieties (Table 1). Interestingly, heparinase Iand heparanase do not have the same HS substrate specificity, and one HSmoiety in particular, IdoA2S-GlcNS, is cleaved by heparinase I but notheparanase (Table 2). Our PAH gene expression data also revealedmarkedly elevated levels of the heparan sulfate 2-O-sulfotransferase 1(HS2ST1) and heparan sulfate 6-O-sulfotransferase 3 (HS6ST2) genes,which encode the HS2ST1 and HS6ST3 enzymes and are necessary forsynthesis of the HS moieties resistant to heparanase (Table 1).

TABLE 1 PAH Gene Expression Data Fold Fold Fold Fold Change ChangeChange Change Gene Day 7/ Day 21/ Day 60/ Day 180/ Symbol Name Base BaseBase Base HPSE Heparanase 1.59 13.24 12.75 2.84 HS2ST1 Heparan 22.4093.98 26.63 140.44 sulfate 2-O-sulfo- transferase 1 HS6ST3 Heparan 1.1221.53 6.33 2.70 sulfate 6-O-sulfo- transferase 3

Heparanase expression was shown to be upregulated in our PAH geneexpression data. Since CAR has demonstrated selective homing in multiplemodels of PAH and it is known that CAR binding and internalizationrequires heparan sulfate receptors on target cell surfaces, CAR is mostlikely binding to a HS moiety that is resistant to heparanase. In arecent study, three HS moieties were shown to be resistant to heparanase(Peterson et al. 2010), but only one of the three is cleaved byheparinase I (Wei et al. 2005), an enzyme which blocks CARinternalization (Jarvinen et al. 2007). Based on this enzymespecificity, we identify IdoA2S-GlcNS as a putative HS moiety to whichCAR binds.

TABLE 2 Comparison of heparan sulfate substrate specificity Heparansulfate moiety Heparinase I cleavage Heparanase cleavage (below) (EC4.2.2.7) (EC 3.2.1.166) GlcA-GlcNAc6S No No GlcA-GlcNS No NoIdoA2S-GlcNS Yes No

One possible mechanism by which CAR could facilitate the selectiveuptake of co-administered drugs is through heparan sulfate-mediatedmacropinocytosis (FIG. 5). Macropinocytosis is a non-clathrin,non-caveolin, lipid raft-dependent form of endocytosis that allows forthe regulated internalization of extracellular solute molecules. Studieshave described the role of heparan sulfate as the receptor for lipidraft-dependent macropinocytotic internalization (Fan et al. 2007), andmacropinocytosis has also been shown to underly the internalization ofother cationic cell-penetrating peptides (Lim et al. 2011; Kaplan et al.2005; Nakase et al. 2004). Heparan sulfate mediated macropinocytosiscould explain CAR's ability to increase the localized concentration ofco-administered drugs without requiring the drugs to be conjugated toCAR.

Detailed description of CAR peptide binding and internalizationmechanism of action is shown in FIG. 3. Specifically, healthy glycocalyxlocated on endothelial cell surface facing bloodstream are shown (FIG.3a ). Due to the full, in-tack glycocalyx layer, CAR cannot access itsunique heparan sulfate receptors. Despite some drug molecules passivelydiffusing through the plasma membrane, the majority of drug will not beinternalized into the healthy cell. Upon PAH injury, heparanaseexpression levels increase, resulting in selective enzymatic cleavage ofsome heparan sulfate chains and modification of the glycocalyx (FIG. 3b). HS variants resistant to heparanase cleavage remain in-tact andaccessible to CAR, allowing CAR to bind to its HS receptors. Next is theinitiation of heparan sulfate-mediated macropinocytosis (FIG. 3c ).Binding of CAR to its HS receptors trigger lipid raft formation andmembrane ruffling, causing an inward folding of the plasma membrane andengulfment of surrounding extracellular components (like CAR and drugmolecules). Vesicles (called macropinosomes) containing CAR and drugmolecules are formed and internalized into the cell (FIG. 3d ). Finally,the reduced intracellular pH causes the macropinosome to dissociate,releasing its contents (CAR and drug) into the diseased cell (FIG. 3e ).

CONCLUSIONS

These data identify a specific HS moiety (IdoA2S-GlcNS) as a possiblereceptor for CAR that could be present in pulmonary hypertensivetissues, in which most other HS moieties have been cleaved by highlevels of heparanase. We further hypothesize that heparansulfate-mediated macropinocytosis could be a plausible mechanism bywhich CAR binding could promote the internalization of co-administeredcompounds. Experiments are currently underway to test and refine thesehypotheses, while CAR is being developed as a therapeutic adjuvant forPAH.

Abbreviations

CAR—a 9 amino acid cyclic peptide CARSKNKDC (where the amino acidsC=cysteine, A=alanine, R=arginine, S=serine, K=lysine, N=asparagine,D=aspartic acid)TAT—trans-activator of transcription proteinPAH—pulmonary arterial hypertensionGTx—gene therapyEC—enzyme classificationHIV—human immunodeficiency virusMFN2—mitofusion-2 geneHPSE—heparanaseHS—heparan sulfateHS2ST1—heparan sulfate 2-O-sulfotransferase 1 geneRNA—ribonucleic acidmPAP—mean pulmonary arterial pressuremmHG—millimeters of mercurycDNA—complementary deoxyribonucleic acid (DNA)MFN2-CAR—mitofusion-2 gene therapy combined with CAR peptide(co-administration)VSMC—vascular smooth muscle cellstCAR—truncated CAR (CARSKNK)CAR variants (take from previous patent apps)RV/LV-S—right ventricle to left ventricle plus septum (weight ratio of)Sugen Hypoxia Rats—rats that are given sugen (a vascular endothelialgrowth factor [VEGF] inhibitor), then placed in a hypoxia (10% oxygen)chamberCH-SU Rats—chronic hypoxia-sugen ratsSMP—selective macropinocytosis promoter

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I claim:
 1. A method for diagnosing the health status of an individualsuffering from Pulmonary Arterial Hypertension (PAH), the methodcomprising: a) obtaining a sample from an individual suffering from PAH;b) measuring heparanase and heparan sulfate levels in the sampleobtained in step a); c) determining the health status of the individualbased on the heparanase and heparan sulfate levels obtained in step b.2. The method of claim 1, wherein the sample is selected from the groupconsisting of tissue, blood and urine.
 3. The method of claim 2, whereinthe sample is a blood sample.
 4. The method of claim 2, wherein the sameis a urine sample.
 5. A method for increasing the localized efficacy ofgene therapy in an individual suffering from a disease byco-administering a therapeutically effective amount of a compositionconsisting of: 1) at least one cell-penetrating peptide; and 2) at leastone other therapeutic agent, wherein at least one compound of thecomposition induces increased macropinocytosis of diseased cells.
 6. Themethod of claim 5, wherein the disease is further characterized bytissue with increased heparanase expression.
 7. The method of claim 6,wherein the disease is selected from the group consisting of pulmonaryhypertension (PAH), interstitial lung disease, acute lung injury (ALI),acute respiratory distress syndrome (ARDS), atherosclerosis, sepsis,septic shock, sarcoidosis of the lung, diabetes, asthma, ankylosingspondylitis, psoriasis, diseases of the endometrium, pulmonarymanifestations of connective tissue diseases, including systemic lupuserythematosus, rheumatoid arthritis, scleroderma, and polymyositis,dermatomyositis, bronchiectasis, asbestosis, berylliosis, silicosis,Histiocytosis X, pneumotitis, smoker's lung, bronchiolitis obliterans,the prevention of lung scarring due to tuberculosis and pulmonaryfibrosis, other fibrotic diseases such as myocardial infarction,endomyocardial fibrosis, mediastinal fibrosis, myelofibrosis,retroperitoneal fibrosis, progressive massive fibrosis, pneumoconiosis,nephrogenic systemic fibrosis, keloid, arthrofibrosis, adhesivecapsulitis, radiation fibrosis, fibrocystic breast condition, livercirrhosis, hepatitis, liver fibrosis, nonalcoholic fatty liver disease,nonalcoholic steatohepatitis, sarcoidosis of the lymph nodes, or otherorgans, inflammatory bowel disease, Crohn's disease, ulcerative colitis,primary biliary cirrhosis, pancreatitis, interstitial cystitis, chronicobstructive pulmonary disease, pneumoconiosis, autoimmune diseases,cancer, angiogenic diseases, wound healing, erectile dysfunction,chronic kidney disease, infections, trauma injuries and systemicconnective tissue diseases including systemic lupus erythematosus,rheumatoid arthritis, psoriatic arthritis, juvenile idiopathic arthritisscleroderma, polymyositis, and dermatomyositis.
 8. The method of claim7, wherein the disease is PAH.
 9. The method of claim 5, wherein thecell-penetrating peptide is selected from the group consisting of CAR(SEQ ID NO: 1), tCAR (SEQ ID NO: 2) or a CAR variant with at least 60%binding affinity to IdoA2s-GlcNS.
 10. The method of claim 9, wherein thecell-penetrating peptide is CAR.
 11. The method of claim 9, wherein thecell-penetrating peptide is tCAR.
 12. The method of claim 9, wherein thecell-penetrating peptide is a CAR variant with at least 60% bindingaffinity to IdoA2s-GlcNS.
 13. The method of claim 9, wherein thetherapeutic agent is selected from the group consisting of smallmolecules, polypeptides, peptides, peptidomimetics, nucleicacid-molecules, cells and viruses.